From 4b2a3789cd7ba15ac41f32f6179bcc1665cb8e47 Mon Sep 17 00:00:00 2001
From: ljmesi <37740329+ljmesi@users.noreply.github.com>
Date: Tue, 3 May 2022 11:03:48 +0200
Subject: [PATCH] Update default values for host removal parameters

---
 nextflow.config | 24 ++++++++++++------------
 1 file changed, 12 insertions(+), 12 deletions(-)

diff --git a/nextflow.config b/nextflow.config
index 04273f1..95daba9 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -81,18 +81,18 @@ params {
     save_runmerged_reads        = false
 
     // Host Removal
-    perform_shortread_hostremoval      = false
-    shortread_hostremoval_reference    = null
-    shortread_hostremoval_index        = null
-    longread_hostremoval_index         = null
-    save_hostremoval_index             = false
-    save_hostremoval_mapped            = false
-    save_hostremoval_unmapped          = false
-    save_minimap2_hostremoval_index    = false
-    save_minimap2_hostremoval_mapped   = false
-    save_minimap2_hostremoval_unmapped = false
-    save_samtools_unmapped_bam         = false
-    save_minimap2_unmapped_fq          = false
+    perform_shortread_hostremoval          = false
+    shortread_hostremoval_reference        = null
+    shortread_hostremoval_index            = null
+    save_hostremoval_index                 = false
+    save_hostremoval_mapped                = false
+    save_hostremoval_unmapped              = false
+    longread_hostremoval_index             = null
+    save_minimap2_hostremoval_index        = false
+    save_minimap2_hostremoval_mapped       = false
+    save_samtools_unmapped_bam             = false
+    save_minimap2_unmapped_fq              = false
+
 
     // MALT
     run_malt                   = false